of phylogenesis the ultimate origination of new biological forms during the

of the origin of biological information exposes a deficiency in the

Match 2 (1):
Reference (000556 .. 000590, of 13533):

Subject (008821 .. 008856, of 28080):

the situation starting in the 1970s many biologists began questioning its neo Darwinism s adequacy in explaining evolution Genetics might be adequate for explaining microevolution but microevolutionary changes in gene frequency were not seen as

Synthesis is a remarkable achievement However starting in the 1970s many biologists began questioning its adequacy in explaining evolution Genetics might be adequate for explaining microevolution but microevolutionary changes in gene frequency were not seen as

Match 3 (1):
Reference (000591 .. 000623, of 13533):

Subject (008904 .. 008937, of 28080):

able to turn a reptile into a mammal or to convert a fish into an amphibian Microevolution looks at adaptations that concern the survival of the fittest not the arrival of the fittest

able to turn a reptile into a mammal or to convert a fish into an amphibian Microevolution looks at adaptations that concern only the survival of the fittest not the arrival of the fittest

Match 4 (1):
Reference (000853 .. 000862, of 13533):

Subject (020356 .. 020366, of 28080):

of the origin of biological form and information during the

of the origin of biological information exposes a deficiency in the

Match 5 (1):
Reference (000999 .. 001010, of 13533):

Subject (000571 .. 000587, of 28080):

time at least nineteen and perhaps as many as thirty five phyla

time During this event at least nineteen and as many as thirty five of forty total phyla

Match 6 (1):
Reference (001112 .. 001140, of 13533):

Subject (001005 .. 001035, of 28080):

To say that the fauna of the Cambrian period appeared in a geologically sudden manner also implies the absence of clear transitional intermediate forms connecting Cambrian animals with simpler

To say that the fauna of the Cambrian period appeared in a geologically sudden manner also implies the absence of clear transitional intermediates connecting the complex Cambrian animals with those simpler

Match 7 (1):
Reference (001789 .. 001823, of 13533):

Subject (002957 .. 002991, of 28080):

information In classical Shannon information theory the amount of information in a system is also inversely related to the probability of the arrangement of constituents in a system or the characters along a communication channel

in biology In classical Shannon information theory the amount of information in a system is inversely related to the probability of the arrangement of constituents in a system or the characters along a communication channel

Match 8 (1):
Reference (001826 .. 001897, of 13533):

Subject (002993 .. 003061, of 28080):

The more improbable or complex the arrangement the more Shannon information or information carrying capacity a string or system possesses Since the 1960s mathematical biologists have realized that Shannon s theory could be applied to the analysis of DNA and proteins to measure the information carrying capacity of these macromolecules Since DNA contains the assembly instructions for building proteins the information processing system in the cell represents a kind of communication channel

The more improbable or complex the arrangement the more Shannon information or information carrying capacity a string or system possesses Since the 1960s mathematical biologists have realized that Shannon s theory could be applied to the analysis of DNA and proteins to measure their information carrying capacity Since DNA contains the assembly instructions for building proteins the information processing system in the cell represents a kind of communication channel

Match 9 (1):
Reference (001911 .. 001920, of 13533):

Subject (003086 .. 003097, of 28080):

bases Since each of the four bases has a roughly

a linear array Since each of the four bases has a roughly

Match 10 (1):
Reference (001911 .. 002032, of 13533):

Subject (003086 .. 003210, of 28080):

bases Since each of the four bases has a roughly equal chance of occurring at each site along the spine of the DNA molecule biologists can calculate the probability and thus the information carrying capacity of any particular sequence n bases long The ease with which information theory applies to molecular biology has created confusion about the type of information that DNA and proteins possess Sequences of nucleotide bases in DNA or amino acids in a protein are highly improbable and thus have large information carrying capacities But like meaningful sentences or lines of computer code genes and proteins are also specified with respect to function Just as the meaning of a sentence depends upon the specific arrangement of the letters in

a linear array Since each of the four bases has a roughly equiprobable chance of occurring at each site along the spine of the DNA molecule biologists can calculate the probability and thus the information carrying capacity of any particular sequence n bases long The ease with which information theory applies to molecular biology has created confusion about the type of information that DNA and proteins possess Sequences of nucleotide bases in DNA or amino acids in a protein are highly improbable and thus have a large information carrying capacity But like meaningful sentences or lines of computer code genes and proteins are also specified with respect to function Just as the meaning of a sentence depends upon the specific arrangement of the letters in

Match 11 (1):
Reference (001911 .. 002054, of 13533):

Subject (003086 .. 003235, of 28080):

bases Since each of the four bases has a roughly equal chance of occurring at each site along the spine of the DNA molecule biologists can calculate the probability and thus the information carrying capacity of any particular sequence n bases long The ease with which information theory applies to molecular biology has created confusion about the type of information that DNA and proteins possess Sequences of nucleotide bases in DNA or amino acids in a protein are highly improbable and thus have large information carrying capacities But like meaningful sentences or lines of computer code genes and proteins are also specified with respect to function Just as the meaning of a sentence depends upon the specific arrangement of the letters in a sentence so too does the function of a gene sequence depend upon the specific arrangement of the nucleotide bases in a

a linear array Since each of the four bases has a roughly equiprobable chance of occurring at each site along the spine of the DNA molecule biologists can calculate the probability and thus the information carrying capacity of any particular sequence n bases long The ease with which information theory applies to molecular biology has created confusion about the type of information that DNA and proteins possess Sequences of nucleotide bases in DNA or amino acids in a protein are highly improbable and thus have a large information carrying capacity But like meaningful sentences or lines of computer code genes and proteins are also specified with respect to function Just as the meaning of a sentence depends upon the specific arrangement of the letters in the sentence so too does the function of a gene sequence depend upon the specific arrangement of the nucleotide bases in the gene Thus as

Match 12 (1):
Reference (002057 .. 002080, of 13533):

Subject (003239 .. 003262, of 28080):

molecular biologists beginning with Crick equated information not only with complexity but also with specificity where specificity or specified has meant necessary to function

molecular biologists beginning with Francis Crick have equated information not only with complexity but also with specificity where specificity has meant necessary to function

Match 13 (1):
Reference (002162 .. 002178, of 13533):

Subject (003127 .. 003144, of 28080):

function The ease with which information theory applies to molecular biology has also created confusion about the

n bases long The ease with which information theory applies to molecular biology has created confusion about the

Match 14 (1):
Reference (002407 .. 002418, of 13533):

Subject (003732 .. 003752, of 28080):

Cambrian explosion represents a remarkable jump in the specified complexity or complex

Cambrian explosion represents a remarkable jump in the specified information or specified complexity of the biological world FIGURE 10 Biological Complexity

Match 15 (1):
Reference (002413 .. 002425, of 13533):

Subject (003281 .. 003291, of 28080):

in the specified complexity or complex specified information CSI of the biological world

in the specified complexity or specified information of the biological world

Match 16 (1):
Reference (002430 .. 002440, of 13533):

Subject (002733 .. 002747, of 28080):

years the biological realm included little more than bacteria and algae

s history the biological realm included little more than unicellular bacteria and blue green algae

the Cambrian explosion represents a steep climb up the biology complexity

Match 19 (1):
Reference (002591 .. 002604, of 13533):

Subject (003339 .. 003353, of 28080):

Functionally more complex animals require more cell types to perform their more diverse functions

Functionally more complex animal forms require more cell types to perform their more diverse functions

Match 20 (1):
Reference (002613 .. 002659, of 13533):

Subject (003457 .. 003504, of 28080):

proteins New proteins in turn require new genetic information Thus an increase in the number of cell types implies at a minimum a considerable increase in the amount of specified genetic information Molecular biologists have recently estimated that a minimally complex single celled organism would require between

proteins in turn require new genetic information encoded in DNA Thus an increase in the number of cell types implies at a minimum a considerable increase in the amount of specified genetic information Molecular biologists have recently estimated that a minimally complex single celled organism would require between

Match 21 (1):
Reference (002659 .. 002674, of 13533):

Subject (003520 .. 003535, of 28080):

between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life

between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life

Match 22 (1):
Reference (002677 .. 002698, of 13533):

Subject (003537 .. 003558, of 28080):

More complex single cells might require upward of a million base pairs Yet to build the proteins necessary to sustain a complex

More complex single cells might require upward of 1 million base pairs Yet to build the proteins necessary to sustain a complex

Match 23 (1):
Reference (002713 .. 002724, of 13533):

Subject (003571 .. 003581, of 28080):

genome size of a modern arthropod the fruitfly Drosophila melanogaster is approximately

genome size of the fly Drosophila melanogaster an arthropod is approximately

Match 24 (1):
Reference (002737 .. 002756, of 13533):

Subject (003608 .. 003627, of 28080):

Transitions from a single cell to colonies of cells to complex animals represent significant and in principle measurable increases in

transitions from a single cell to colonies of cells to complex animals represent significant and in principle measurable increases in

Match 25 (1):
Reference (002936 .. 002958, of 13533):

Subject (014998 .. 015022, of 28080):

Many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins

a number of scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins

Match 26 (1):
Reference (002962 .. 002980, of 13533):

Subject (015026 .. 015044, of 28080):

derives from consideration of the extreme improbability and specificity of functional genes and proteins A typical gene contains over

derived from consideration of the extreme improbability and specificity of functional genes and proteins A typical gene contains over

Match 27 (1):
Reference (002987 .. 002997, of 13533):

Subject (015052 .. 015062, of 28080):

any specific arrangement of four nucleotide bases of length n there

any specific arrangement of four nucleotide bases of length n there

Match 28 (1):
Reference (002999 .. 003075, of 13533):

Subject (015064 .. 015143, of 28080):

a corresponding number of possible arrangements of bases 4n For any protein there are 20n possible arrangements of protein forming amino acids A gene 999 bases in length represents one of 4999 possible nucleotide sequences a protein of 333 amino acids is one of 20333 possibilities Since the 1960s some biologists have thought functional proteins to be rare among the set of possible amino acid sequences Some have used an analogy with human language to illustrate why

a corresponding number of 4n possible arrangements of bases For any protein there are 20n possible arrangements of protein forming amino acids A gene of 999 bases in length represents one of 4999 possible nucleotide sequences a protein of 333 amino acids one of 20333 possibilities Since the 1960s biologists have generally thought functional proteins to be rare among the set of possible amino acid sequences of corresponding length Some have used an analogy with human language to illustrate why

Match 29 (1):
Reference (003093 .. 003157, of 13533):

Subject (015154 .. 015218, of 28080):

sentences are extremely rare among the set of possible combinations of English letters especially as sequence length grows The ratio of meaningful 12 letter words to 12 letter sequences is 1 1014 the ratio of 100 letter sentences to possible 100 letter strings is 1 10100 Further Denton shows that most meaningful sentences are highly isolated from one another in the space of possible combinations

sentences are extremely rare among the set of possible combinations of English letters especially as sequence length grows The ratio of meaningful 12 letter words to 12 letter sequences is 1 1014 the ratio of 100 letter sentences to possible 100 letter strings is 1 10100 Further Denton shows that most meaningful sentences are highly isolated from one another in the space of possible combinations

Match 30 (1):
Reference (003159 .. 003224, of 13533):

Subject (015220 .. 015284, of 28080):

that random substitutions of letters will after a very few changes inevitably degrade meaning Apart from a few closely clustered sentences accessible by random substitution the overwhelming majority of meaningful sentences lie probabilistically speaking beyond the reach of random search Denton 1986 301 324 and others have argued that similar constraints apply to genes and proteins They have questioned whether an undirected search via mutation and

that random substitutions of letters will after a very few changes inevitably degrade meaning Apart from a few closely clustered sentences accessible by random substitution the overwhelming majority of meaningful sentences lie probabilistically speaking beyond the reach of random search Denton and others have argued that similar constraints apply to genes They have questioned therefore whether an undirected search via mutation selection would have a

Match 31 (1):
Reference (003159 .. 003246, of 13533):

Subject (015220 .. 015300, of 28080):

that random substitutions of letters will after a very few changes inevitably degrade meaning Apart from a few closely clustered sentences accessible by random substitution the overwhelming majority of meaningful sentences lie probabilistically speaking beyond the reach of random search Denton 1986 301 324 and others have argued that similar constraints apply to genes and proteins They have questioned whether an undirected search via mutation and selection would have a reasonable chance of locating new islands of function representing fundamentally new genes or proteins within the time available

that random substitutions of letters will after a very few changes inevitably degrade meaning Apart from a few closely clustered sentences accessible by random substitution the overwhelming majority of meaningful sentences lie probabilistically speaking beyond the reach of random search Denton and others have argued that similar constraints apply to genes They have questioned therefore whether an undirected search via mutation selection would have a reasonable chance of locating new islands of function representing fundamentally new genes or proteins within available

Match 32 (1):
Reference (003253 .. 003274, of 13533):

Subject (015303 .. 015324, of 28080):

Some have also argued that alterations in sequencing would likely result in loss of protein function before fundamentally new function could arise

Some have also argued that alterations in sequencing would likely result in loss of protein function before fundamentally new function could arise

Match 33 (1):
Reference (003285 .. 003349, of 13533):

Subject (015330 .. 015392, of 28080):

genes and proteins are sensitive to functional loss as a result of sequence change nor the extent to which functional proteins are isolated within sequence space has been fully known Recently experiments in molecular biology have shed light on these questions A variety of mutagenesis techniques have shown that proteins and thus the genes that produce them are indeed highly specified relative to biological function

genes and proteins to functional loss as the result of sequence change nor the extent to which functional proteins are isolated within sequence space has been fully known Recently experiments in molecular biology have shed light on these questions A variety of mutagenesis techniques have shown that proteins and thus the genes that produce them are indeed highly specified relative to biological function

Match 34 (1):
Reference (003287 .. 003297, of 13533):

Subject (015532 .. 015546, of 28080):

proteins are sensitive to functional loss as a result of sequence

proteins are highly sensitive to functional loss as a result of alterations in the sequencing

Match 35 (1):
Reference (003361 .. 003381, of 13533):

Subject (015394 .. 015414, of 28080):

Mutagenesis research tests the sensitivity of proteins and by implication DNA to functional loss as a result of alterations in sequencing

Mutagenesis research tests the sensitivity of proteins and by implication DNA to functional loss as a result of alterations in sequencing

Match 36 (1):
Reference (003452 .. 003461, of 13533):

Subject (015496 .. 015506, of 28080):

multiple as opposed to single position amino acid substitutions inevitably

multiple as opposed to single amino acid substitutions generally result in

Match 37 (1):
Reference (003462 .. 003529, of 13533):

Subject (015505 .. 015575, of 28080):

result in loss of protein function even when these changes occur at sites that allow variation when altered in isolation Cumulatively these constraints imply that proteins are highly sensitive to functional loss as a result of alterations in sequencing and that functional proteins represent highly isolated and improbable arrangements of amino acids arrangements that are far more improbable in fact than would be likely to arise by chance

result in rapid loss of protein function even when these changes occur at sites that allow variation when altered in isolation 93 Cumulatively these constraints imply that proteins are highly sensitive to functional loss as a result of alterations in the sequencing and that functional proteins represent highly isolated and improbable arrangements of amino acids arrangements that are far more improbable in fact than would be likely to arise by chance

Match 38 (1):
Reference (003566 .. 003578, of 13533):

Subject (015583 .. 015595, of 28080):

Of course neo Darwinists do not envision a completely random search through the

Of course neo Darwinists do not envision a completely random search through the

Match 39 (1):
Reference (003591 .. 003777, of 13533):

Subject (015603 .. 015790, of 28080):

natural selection acting to preserve small advantageous variations in genetic sequences and their corresponding protein products Dawkins 1996 for example likens an organism to a high mountain peak He compares climbing the sheer precipice up the front side of the mountain to building a new organism by chance He acknowledges that his approach up Mount Improbable will not succeed Nevertheless he suggests that there is a gradual slope up the backside of the mountain that could be climbed in small incremental steps In his analogy the backside climb up Mount Improbable corresponds to the process of natural selection acting on random changes in the genetic text What chance alone cannot accomplish blindly or in one leap selection acting on mutations can accomplish through the cumulative effect of many slight successive steps Yet the extreme specificity and complexity of proteins presents a difficulty not only for the chance origin of specified biological information i e for random mutations acting alone but also for selection and mutation acting in concert Indeed mutagenesis experiments cast doubt on each of the two scenarios by which neo Darwinists envisioned new information arising

natural selection acting to preserve small advantageous variations in genetic sequences and their corresponding protein products Richard Dawkins for example likens an organism to a high mountain peak 95 He compares climbing the sheer precipice up the front side of the mountain to building a new organism by chance He acknowledges that this approach up Mount Improbable will not succeed Nevertheless he suggests that there is a gradual slope up the backside of the mountain that could be climbed in small incremental steps In his analogy the backside up Mount Improbable corresponds to the process of natural selection acting on random changes in the genetic text What chance alone cannot accomplish blindly or in one leap selection acting on mutations can accomplish through the cumulative effect of many slight successive steps Yet the extreme specificity and complexity of proteins present a diffi culty not only for the chance origin of specified biological information that is for random mutations acting alone but also for selection and mutation acting in concert Indeed mutagenesis experiments cast doubt on each of the two scenarios by which neo Darwinists envision new information arising

Match 40 (1):
Reference (003790 .. 003862, of 13533):

Subject (015799 .. 015872, of 28080):

Darwinism new functional genes either arise from non coding sections in the genome or from preexisting genes Both scenarios are problematic In the first scenario neo Darwinists envision new genetic information arising from those sections of the genetic text that can presumably vary freely without consequence to the organism According to this scenario non coding sections of the genome or duplicated sections of coding regions can experience a protracted period of neutral evolution

Darwinists either new functional genes arise from noncoding sections in the genome or functional genes arise from preexisting genes Both scenarios are problematic In the first scenario neo Darwinists envision new genetic information arising from those sections of the genetic text that can presumably vary freely without consequence to the organism According to this scenario noncoding sections of the genome or duplicated sections of coding regions can experience a protracted period of neutral evolution

Match 41 (1):
Reference (003794 .. 003956, of 13533):

Subject (015800 .. 015968, of 28080):

either arise from non coding sections in the genome or from preexisting genes Both scenarios are problematic In the first scenario neo Darwinists envision new genetic information arising from those sections of the genetic text that can presumably vary freely without consequence to the organism According to this scenario non coding sections of the genome or duplicated sections of coding regions can experience a protracted period of neutral evolution Kimura 1983 during which alterations in nucleotide sequences have no discernible effect on the function of the organism Eventually however a new gene sequence will arise that can code for a novel protein At that point natural selection can favor the new gene and its functional protein product thus securing the preservation and heritability of both This scenario has the advantage of allowing the genome to vary through many generations as mutations search the space of possible base sequences The scenario has an overriding problem however the size of the combinatorial space i e

either new functional genes arise from noncoding sections in the genome or functional genes arise from preexisting genes Both scenarios are problematic In the first scenario neo Darwinists envision new genetic information arising from those sections of the genetic text that can presumably vary freely without consequence to the organism According to this scenario noncoding sections of the genome or duplicated sections of coding regions can experience a protracted period of neutral evolution in which alterations in nucleotide sequences have no discernible effect on the function of the organism Eventually however a new gene sequence will arise that can code for a novel protein At that point natural selection can favor the new gene and its functional protein product thus securing the preservation and heritability of both This scenario has the advantage of allowing the genome to vary through many generations as mutations search the space of possible base sequences The scenario has an overriding problem however the size of the combinatorial space and the extreme rarity of the

Match 42 (1):
Reference (003964 .. 004022, of 13533):

Subject (015963 .. 016017, of 28080):

and the extreme rarity and isolation of the functional sequences within that space of possibilities Since natural selection can do nothing to help generate new functional sequences but rather can only preserve such sequences once they have arisen chance alone random variation must do the work of information generation that is of finding the exceedingly rare functional sequences within

and the extreme rarity of the functional sequences within that space of possibilities Since natural selection can do nothing to help generate new functional sequences but rather can only preserve such sequences once they have arisen chance alone random variation must do the work of information generation that is of finding rare functional sequences within

Match 43 (1):
Reference (004025 .. 004043, of 13533):

Subject (016020 .. 016038, of 28080):

of combinatorial possibilities Yet the probability of randomly assembling or finding in the previous sense a functional sequence is

of combinatorial possibilities Yet the probability of randomly assembling or finding in the previous sense a functional sequence is

Match 44 (1):
Reference (004054 .. 004077, of 13533):

Subject (016051 .. 016078, of 28080):

suggest that the probability of attaining at random the correct sequencing for a short protein 100 amino acids long is about 1 in 1065

s mutagenesis experiments imply that the probability of attaining at random the correct sequencing for a short protein 100 amino acids long is about 1 chance in 1065

Match 45 (1):
Reference (004207 .. 004217, of 13533):

Subject (015119 .. 015130, of 28080):

to b the whole set of possible amino acids sequences of

to be rare among the set of possible amino acid sequences of

Match 46 (1):
Reference (004239 .. 004248, of 13533):

Subject (015115 .. 015131, of 28080):

a functional protein among the possible amino acid sequences corresponding

generally thought functional proteins to be rare among the set of possible amino acid sequences of corresponding

Match 47 (1):
Reference (004259 .. 004318, of 13533):

Subject (016099 .. 016158, of 28080):

Other considerations imply additional improbabilities First new Cambrian animals would require proteins much longer than 100 residues to perform many necessary specialized functions Ohno 1996 has noted that Cambrian animals would have required complex proteins such as lysyl oxidase in order to support their stout body structures Lysyl oxidase molecules in extant organisms comprise over 400 amino acids These molecules

Other considerations imply additional improbabilities First new Cambrian animals would require proteins much longer than 100 residues to perform necessary specialized functions Susumu Ohno has noted that Cambrian animals would have required complex proteins such as lysyl oxidase in order to support their stout body structures 98 Lysyl oxidase molecules in extant organisms comprise over 400 amino acids These molecules

Match 48 (1):
Reference (004327 .. 004352, of 13533):

Subject (016165 .. 016193, of 28080):

specified Reasonable extrapolation from mutagenesis experiments done on shorter protein molecules suggests that the probability of producing functionally sequenced proteins of this length at random is

specified arrangements of matter Reasonable extrapolation from mutagenesis experiments done on shorter protein molecules suggests that the probability of producing functionally sequenced proteins of this length at random is

Match 49 (1):
Reference (004450 .. 004479, of 13533):

Subject (016263 .. 016292, of 28080):

Third DNA mutation rates are far too low to generate the novel genes and proteins necessary to building the Cambrian animals given the most probable duration of the explosion as

Third DNA mutation rates are far too slow to generate the novel genes and proteins necessary to building the Cambrian animals given the duration of the explosion As Ohno has

Match 50 (1):
Reference (004544 .. 004561, of 13533):

Subject (016388 .. 016405, of 28080):

The selection mutation mechanism faces another probabilistic obstacle The animals that arise in the Cambrian exhibit structures that

The mutation selection mechanism faces another probabilistic obstacle The animals that arise in the Cambrian exhibit structures that

Match 51 (1):
Reference (004565 .. 004721, of 13533):

Subject (016407 .. 016559, of 28080):

many new types of cells each of which would have required many novel proteins to perform their specialized functions Further new cell types require systems of proteins that must as a condition of functioning act in close coordination with one another The unit of selection in such systems ascends to the system as a whole Natural selection selects for functional advantage But new cell types require whole systems of proteins to perform their distinctive functions In such cases natural selection cannot contribute to the process of information generation until after the information necessary to build the requisite system of proteins has arisen Thus random variations must again do the work of information generation and now not simply for one protein but for many proteins arising at nearly the same time Yet the odds of this occurring by chance alone are of course far smaller than the odds of the chance origin of a single gene or protein

many new types of cells each of which would require many novel proteins to perform their specialized functions Further new cell types require systems of proteins that must as a condition of function act in close coordination with one another The unit of selection in such systems ascends to the system as a whole Natural selection selects for functional advantage But new cell types require whole systems of proteins to perform their distinctive functions In such cases natural selection cannot contribute to the process of information generation until after the information necessary to build the requisite system of proteins has arisen Thus random variations must again do the work of information generation and now not simply for one protein but for many proteins arising at nearly the same time Yet the odds of this occurring by chance are far smaller than the odds of the chance origin of a single gene or protein

Match 52 (1):
Reference (004729 .. 004738, of 13533):

Subject (014642 .. 014649, of 28080):

the chance origin of the genetic information necessary to build

the origin of the information necessary to build

Match 53 (1):
Reference (004790 .. 004866, of 13533):

Subject (016583 .. 016661, of 28080):

The neutral theory of evolution which by its own logic prevents natural selection from playing a role in generating genetic information until after the fact relies on entirely too much luck The sensitivity of proteins to functional loss the need for long proteins to build new cell types and animals the need for whole new systems of proteins to service new cell types the probable brevity of the Cambrian explosion relative to mutation rates all suggest the

The neutral theory of evolution which by its own logic prevents natural selection from playing a role in generating genetic information until after the fact relies on entirely too much luck The sensitivity of proteins to functional loss the need for long proteins to build new cell types and animals the need for whole new systems of proteins to service new cell types the brevity of the Cambrian explosion relative to mutation rates all these factors suggest that the

Match 54 (1):
Reference (004870 .. 004881, of 13533):

Subject (014544 .. 014554, of 28080):

implausibility of any scenario for the origination of Cambrian genetic information that

s previous discussion of the origin of genetic information in a

Match 55 (1):
Reference (004887 .. 004949, of 13533):

Subject (016684 .. 016747, of 28080):

unassisted by natural selection Yet the neutral theory requires novel genes and proteins to arise essentially by random mutation alone Adaptive advantage accrues after the generation of new functional genes and proteins Thus natural selection cannot play a role until new information bearing molecules have independently arisen Thus neutral theorists envisioned the need to scale the steep face of a Dawkins style precipice

unassisted by natural selection Yet the neutral theory requires novel genes and proteins to arise essentially by random mutation alone Adaptive advantage accrues after the generation of new functional genes and proteins Thus natural selection cannot play a role until new information bearing molecules have independently arisen Thus the neutral theory envisions the need to scale the steep face of a Dawkins style precipice

Match 56 (1):
Reference (004951 .. 004984, of 13533):

Subject (016749 .. 016783, of 28080):

which there is no gradually sloping backside a situation that by Dawkins own logic is probabilistically untenable In the second scenario neo Darwinists envisioned novel genes and proteins arising by numerous successive mutations in

which there is no gradually sloping backside a situation that by Dawkins s own logic is probabilistically untenable In the second scenario neo Darwinists envision novel genes and proteins arising by numerous successive mutations in

Match 57 (1):
Reference (004986 .. 005019, of 13533):

Subject (016785 .. 016819, of 28080):

preexisting genetic text that codes for proteins To adapt Dawkins s metaphor this scenario envisions gradually climbing down one functional peak and then ascending another Yet mutagenesis experiments again suggest a difficulty Recent experiments

preexisting genetic text that codes for proteins To adapt Dawkins s metaphor slightly this scenario envisions gradually climbing down one functional peak and then ascending another Yet mutagenesis experiments again suggest a difficulty Recent experiments

Match 58 (1):
Reference (005020 .. 005048, of 13533):

Subject (016827 .. 016853, of 28080):

show that even when exploring a region of sequence space populated by proteins of a single fold and function most multiple position changes quickly lead to loss of function

show that even when exploring a region of sequence space populated by proteins of a single function most multiple position changes quickly lead to loss of function

Match 59 (1):
Reference (005051 .. 005065, of 13533):

Subject (016855 .. 016867, of 28080):

Yet to turn one protein into another with a completely novel structure and function requires

Yet to turn one protein into another with a completely novel function requires

Match 60 (1):
Reference (005132 .. 005161, of 13533):

Subject (016878 .. 016908, of 28080):

Axe s results imply that in all probability random searches for novel proteins through sequence space will result in functional loss long before any novel functional protein will emerge Blanco

Axe s results imply that in all probability random searches for novel proteins through sequence space will result in functional loss long before any novel functional protein will emerge Francisco Blanco

Match 61 (1):
Reference (005247 .. 005279, of 13533):

Subject (017014 .. 017046, of 28080):

Thus although this second neo Darwinian scenario has the advantage of starting with functional genes and proteins it also has a lethal disadvantage any process of random mutation or rearrangement in the genome

Thus although this second neo Darwinian scenario has the advantage of starting with functional genes and proteins it also has a lethal disadvantage any process of random mutation or rearrangement in the genome

Match 62 (1):
Reference (005300 .. 005348, of 13533):

Subject (017068 .. 017118, of 28080):

sequences confer no survival advantage on their host organisms Natural selection favors only functional advantage It cannot select or favor nucleotide sequences or polypeptide chains that do not yet perform biological functions and still less will it favor sequences that efface or destroy preexisting function Evolving genes and proteins

sequences would thus confer no survival advantage on their host organisms Yet natural selection favors only functional advantage It cannot select or favor nucleotide sequences or polypeptide chains that do not yet perform biological functions still less will it favor sequences that efface or destroy preexisting function Evolving genes and proteins

Match 63 (1):
Reference (005350 .. 005371, of 13533):

Subject (017120 .. 017141, of 28080):

range through a series of nonfunctional intermediate sequences that natural selection will not favor or preserve but will in all probability eliminate

range through a series of nonfunctional intermediate sequences that natural selection will not favor or preserve but will in all probability eliminate

Match 64 (1):
Reference (005378 .. 005407, of 13533):

Subject (017143 .. 017173, of 28080):

When this happens selection driven evolution will cease At this point neutral evolution of the genome unhinged from selective pressure may ensue but as we have seen such a process

When this happens selection driven evolution will cease At this point neutral evolution of the genome unhinged from selective pressure may ensue but as we have already seen such a process

Match 65 (1):
Reference (005413 .. 005543, of 13533):

Subject (017183 .. 017317, of 28080):

even granting cosmic time Thus whether one envisions the evolutionary process beginning with a noncoding region of the genome or a preexisting functional gene the functional specificity and complexity of proteins impose very stringent limitations on the efficacy of mutation and selection In the first case function must arise first before natural selection can act to favor a novel variation In the second case function must be continuously maintained in order to prevent deleterious or lethal consequences to the organism and to allow further evolution Yet the complexity and functional specificity of proteins implies that both these conditions will be extremely difficult to meet Therefore the neo Darwinian mechanism appears to be inadequate to generate the new information present in the novel genes and proteins that arise with the Cambrian animals

even granting a cosmic time scale Thus whether one envisions the evolutionary process beginning with a noncoding region of the genome or a preexisting functional gene the functional specificity and complexity of proteins impose very stringent limitations on the efficacy of mutation and selection In the first case function must arise first before natural selection can act to favor a novel variation In the second case function must be continuously maintained to prevent deleterious or lethal consequences to the organism and to allow for the possibility of further evolution Yet the complexity and functional speci ficity of proteins imply that both these conditions will be extremely diffi cult to meet Therefore the neo Darwinian mechanism appears inadequate to generate the new information present in the novel genes and proteins that arise with the Cambrian animals

Match 66 (1):
Reference (005560 .. 005595, of 13533):

Subject (017335 .. 017370, of 28080):

explain the origin of the Cambrian animals one must account not only for new proteins and cell types but also for the origin of new body plans Within the past decade developmental biology has dramatically advanced

explain the origin of the Cambrian animals one must account not only for new proteins and cell types but also for the origin of new body plans Within the past decade developmental biology has dramatically advanced

Match 67 (1):
Reference (005597 .. 005615, of 13533):

Subject (017443 .. 017461, of 28080):

understanding of how body plans are built during ontogeny In the process it has also uncovered a profound difficulty

understanding of how body plans are built during ontogeny In the process it has also uncovered a profound difficulty

Match 68 (1):
Reference (005621 .. 005655, of 13533):

Subject (017472 .. 017510, of 28080):

change in organisms requires attention to timing Mutations in genes that are expressed late in the development of an organism will not affect the body plan Mutations expressed early in development however could conceivably produce

changes in the form of organisms requires attention to timing Mutations in genetic material that are expressed late in the development of an organism will not affect the body plan Mutations expressed early in development however could conceivably produce

Match 69 (1):
Reference (005662 .. 005681, of 13533):

Subject (017520 .. 017539, of 28080):

Thus events expressed early in the development of organisms have the only realistic chance of producing large scale macroevolutionary change

Thus events expressed early in the development of organisms have the only realistic chance of producing large scale macroevolutionary change

Match 70 (1):
Reference (005702 .. 005718, of 13533):

Subject (017555 .. 017571, of 28080):

Yet recent studies in developmental biology make clear that mutations expressed early in development typically have deleterious

Yet recent studies in developmental biology make clear that mutations expressed early in development typically have deleterious

Match 71 (1):
Reference (005723 .. 005754, of 13533):

Subject (017588 .. 017620, of 28080):

For example when early acting body plan molecules or morphogens such as bicoid which helps to set up the anterior posterior head to tail axis in Drosophila are perturbed development shuts down

For example when early acting body plan molecules or morphogens such as bicoid which helps set up the anterior posterior head to tail axis in the fly Drosophila are perturbed development shuts down

Match 72 (1):
Reference (005766 .. 005837, of 13533):

Subject (017622 .. 017693, of 28080):

The resulting embryos die Moreover there is a good reason for this If an engineer modifies the length of the piston rods in an internal combustion engine without modifying the crankshaft accordingly the engine won t start Similarly processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream For this reason

The resulting embryos die Moreover there is a good reason for this If an engineer modifies the length of the piston rods in an internal combustion engine without modifying the crankshaft accordingly the engine won t start Similarly processes of development are so tightly integrated spatially and temporally that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream For this reason

Match 73 (1):
Reference (005874 .. 005887, of 13533):

Subject (017856 .. 017871, of 28080):

This problem has led to what McDonald 1983 has called a great Darwinian paradox

This problem has led to what geneticist John F McDonald has called a great Darwinian paradox

Match 74 (1):
Reference (005914 .. 005924, of 13533):

Subject (017895 .. 017905, of 28080):

major changes the very stuff of macroevolution apparently do not vary

major changes the very stuff of macroevolution apparently do not vary

Match 75 (1):
Reference (005934 .. 005948, of 13533):

Subject (017990 .. 018004, of 28080):

doesn t need namely viable genetic mutations in DNA expressed late in development do occur

doesn t need namely viable genetic mutations in DNA expressed late in development do occur

that the kind of variations required by neo Darwinism favorable mutations

Match 77 (1):
Reference (006008 .. 006034, of 13533):

Subject (018049 .. 018078, of 28080):

occur Developmental biology has raised another formidable problem for the mutation selection mechanism Embryological evidence has long shown that DNA does not wholly determine morphological form Goodwin

occur Developmental biology has raised another formidable problem for the mutation selection mechanism Embryological evidence has long shown that DNA does not wholly determine morphological form suggesting that mutations in

Match 78 (1):
Reference (006043 .. 006062, of 13533):

Subject (018075 .. 018095, of 28080):

suggesting that mutations in DNA alone cannot account for the morphological changes required to build a new body plan DNA

suggesting that mutations in DNA alone cannot account for the morphological changes required to build a new body plan 112 DNA

Match 79 (1):
Reference (006043 .. 006084, of 13533):

Subject (018075 .. 018114, of 28080):

suggesting that mutations in DNA alone cannot account for the morphological changes required to build a new body plan DNA helps direct protein synthesis 7 It also helps to regulate the timing and expression of the synthesis of various proteins within cells

suggesting that mutations in DNA alone cannot account for the morphological changes required to build a new body plan 112 DNA directs protein synthesis It also helps regulate the timing and expression of the synthesis of various proteins within cells

Match 80 (1):
Reference (006086 .. 006104, of 13533):

Subject (018116 .. 018134, of 28080):

DNA alone does not determine how individual proteins assemble themselves into larger systems of proteins still less does it

DNA alone does not determine how individual proteins assemble themselves into larger systems of proteins still less does it

Instead other factors such as the three dimensional structure and organization of the cell membrane and cytoskeleton

Instead other factors such as the structure and organization of the cell membrane and cytoskeleton

Match 83 (1):
Reference (006149 .. 006161, of 13533):

Subject (018165 .. 018181, of 28080):

play important roles in determining body plan formation during embryogenesis For example the

play important roles in determining developmental pathways that determine body plan formation during embryogenesis For example the

Match 84 (1):
Reference (006163 .. 006202, of 13533):

Subject (018183 .. 018224, of 28080):

and location of the cytoskeleton influence the patterning of embryos Arrays of microtubules help to distribute the essential proteins used during development to their correct locations in the cell Of course microtubules themselves are made of many protein subunits Nevertheless

and location of microtubules in the cytoskeleton influence the patterning of embryos Arrays of microtubules help distribute the essential proteins used during development to their correct location in the cell 114 Of course microtubules themselves are made of many protein subunits Nevertheless

Match 85 (1):
Reference (006216 .. 006226, of 13533):

Subject (018223 .. 018237, of 28080):

subunits in the cell s microtubules are identical to one another

subunits Nevertheless the protein subunits in the cell s microtubules are identical to one another

Match 86 (1):
Reference (006232 .. 006254, of 13533):

Subject (018240 .. 018264, of 28080):

nor the genes that produce them account for the different shape of microtubule arrays that distinguish different kinds of embryos and developmental pathways

nor the genes that produce them account for the different shapes and locations of microtubule arrays that distinguish different kinds of embryos and developmental pathways

Match 87 (1):
Reference (006319 .. 006386, of 13533):

Subject (018301 .. 018368, of 28080):

At a building site builders will make use of many materials lumber wires nails drywall piping and windows Yet building materials do not determine the floor plan of the house or the arrangement of houses in a neighborhood Similarly electronic circuits are composed of many components such as resistors capacitors and transistors But such lower level components do not determine their own arrangement in an integrated circuit Biological

At a building site builders will make use of many materials lumber wires nails drywall piping and windows Yet building materials do not determine the floor plan of the house or the arrangement of houses in a neighborhood Similarly electronic circuits are composed of many components such as resistors capacitors and transistors But such lower level components do not determine their own arrangement in an integrated circuit Biological

Match 88 (1):
Reference (006388 .. 006475, of 13533):

Subject (018370 .. 018455, of 28080):

also depend on hierarchical arrangements of parts Genes and proteins are made from simple building blocks nucleotide bases and amino acids arranged in specific ways Cell types are made of among other things systems of specialized proteins Organs are made of specialized arrangements of cell types and tissues And body plans comprise specific arrangements of specialized organs Yet clearly the properties of individual proteins or indeed the lower level parts in the hierarchy generally do not fully determine the organization of the higher level structures and organizational patterns

also depend on hierarchical arrangements of parts Genes and proteins are made from simple building blocks nucleotide bases and amino acids arranged in specific ways Cell types are made of among other things systems of specialized proteins Organs are made of specialized arrangements of cell types and tissues And body plans comprise specific arrangements of organs Yet clearly the properties of individual proteins or indeed the lower level parts in the hierarchy generally do not determine the organization of the higher level structures and organizational patterns

Match 89 (1):
Reference (006479 .. 006523, of 13533):

Subject (018457 .. 018501, of 28080):

It follows that the genetic information that codes for proteins does not determine these higher level structures either These considerations pose another challenge to the sufficiency of the neo Darwinian mechanism Neo Darwinism seeks to explain the origin of new information form and structure as

It follows therefore that the genetic information that codes for proteins does not determine these higherlevel structures either These considerations pose another challenge to the sufficiency of the neo Darwinian mechanism Neo Darwinism seeks to explain the origin of new information form and structure as

Match 90 (1):
Reference (006479 .. 006573, of 13533):

Subject (018457 .. 018549, of 28080):

It follows that the genetic information that codes for proteins does not determine these higher level structures either These considerations pose another challenge to the sufficiency of the neo Darwinian mechanism Neo Darwinism seeks to explain the origin of new information form and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy namely within the genetic text Yet major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy a level that DNA alone does not determine

It follows therefore that the genetic information that codes for proteins does not determine these higherlevel structures either These considerations pose another challenge to the sufficiency of the neo Darwinian mechanism Neo Darwinism seeks to explain the origin of new information form and structure as the result of selection acting on randomly arising variation at a very low level within the biological hierarchy namely within the genetic text Yet major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy that DNA alone does not determine

Match 91 (1):
Reference (006576 .. 006632, of 13533):

Subject (018551 .. 018607, of 28080):

DNA is not wholly responsible for body plan morphogenesis then DNA sequences can mutate indefinitely without regard to realistic probabilistic limits and still not produce a new body plan Thus the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans including those that first arose in the Cambrian explosion

DNA is not wholly responsible for body plan morphogenesis then DNA sequences can mutate indefinitely without regard to realistic probabilistic limits and still not produce a new body plan Thus the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans including those that first arose in the Cambrian explosion

Match 92 (1):
Reference (007139 .. 007157, of 13533):

Subject (018617 .. 018636, of 28080):

Of course neo Darwinism is not the only evolutionary theory for explaining the origin of novel biological form Kauffman

Of course neo Darwinism is not the only evolutionary model for explaining the origin of novel biological form in an

Match 93 (1):
Reference (007175 .. 007317, of 13533):

Subject (018650 .. 018787, of 28080):

to account for the emergence of new form and presumably the information necessary to generate it Whereas neo Darwinism attempts to explain new form as the consequence of selection acting on random mutation Kauffman suggests that selection acts not mainly on random variations but on emergent patterns of order that self organize via the laws of nature Kauffman 1995 47 92 illustrates how this might work with various model systems in a computer environment In one he conceives a system of buttons connected by strings Buttons represent novel genes or gene products strings represent the law like forces of interaction that obtain between gene products i e proteins Kauffman suggests that when the complexity of the system as represented by the number of buttons and strings reaches a critical threshold new modes of organization can arise in the system for free that is

to account for the emergence of form and presumably the information necessary to generate it Whereas neo Darwinism attempts to explain new form as the consequence of selection acting on random mutation Kauffman suggests that selection acts not mainly on random variations but on emergent patterns of order that self organize via the laws of nature Kauffman illustrates how this might work with various model systems in a computer environment In one he conceives a system of buttons connected by strings Buttons represent novel genes or gene products strings the lawlike forces of interaction that obtain between gene products that is proteins Kauffman suggests that when the complexity of the system as represented by the number of connected buttons and strings reaches a critical threshold new modes of organization can arise in the system for free that is

Match 94 (1):
Reference (007330 .. 007352, of 13533):

Subject (018905 .. 018927, of 28080):

Another model that Kauffman develops is a system of interconnected lights Each light can flash in a variety of states on off twinkling

Another model that Kauffman develops is a system of interconnected lights Each light can flash in a variety of states on off twinkling

Match 95 (1):
Reference (007354 .. 007429, of 13533):

Subject (018931 .. 019010, of 28080):

Since there is more than one possible state for each light and many lights there are a vast number of possible states that the system can adopt Further in his system rules determine how past states will influence future states Kauffman asserts that as a result of these rules the system will if properly tuned eventually produce a kind of order in which a few basic patterns of light activity recur with greater than random frequency

Since there is more than one possible state for each light and many lights there are a vast number of possible states that the system as a whole can adopt Further in his system rules determine how past states will in fluence future states Kauffman asserts that as a result of these rules the system will soon if properly tuned produce a kind of order in which a few basic patterns of light activity recur with greater than random frequency

Match 96 (1):
Reference (007431 .. 007454, of 13533):

Subject (019014 .. 019037, of 28080):

these actual patterns of light activity represent a small portion of the total number of possible states in which the system can reside Kauffman

these actual patterns of light activity represent a small portion of the total number of possible states in which the system can reside Kauffman

Match 97 (1):
Reference (007458 .. 007534, of 13533):

Subject (019039 .. 019114, of 28080):

that self organizational laws might similarly result in highly improbable biological outcomes perhaps even sequences of bases or amino acids within a much larger sequence space of possibilities Do these simulations of self organizational processes accurately model the origin of novel genetic information It is hard to think so First in both examples Kauffman presupposes but does not explain significant sources of preexisting information In his buttons and strings system the buttons represent proteins themselves packets of

that self organizational laws might similarly find highly improbable biological outcomes perhaps even sequences of bases or amino acids within a much larger sequence space of possibilities Do these simulations of self organizational processes accurately model the origin of novel genetic information It s hard to think so First in both examples Kauffman presupposes but does not explain significant sources of preexisting information In his buttons and strings system the buttons represent proteins themselves packets of

Match 98 (1):
Reference (007536 .. 007567, of 13533):

Subject (019116 .. 019149, of 28080):

and the result of preexisting genetic information Where does this information come from Kauffman 1995 doesn t say but the origin of such information is an essential part of what needs to

and the result of preexisting genetic information Where does this information come from Kauffman doesn t say but the origin of such information is an essential part of what needs explanation in the history

Match 99 (1):
Reference (007570 .. 007587, of 13533):

Subject (019147 .. 019163, of 28080):

in the history of life Similarly in his light system the order that allegedly arises for for free

in the history of life Similarly in his light system the order that allegedly arises for free

Match 100 (1):
Reference (007588 .. 007616, of 13533):

Subject (019174 .. 019201, of 28080):

actually arises only if the programmer of the model system tunes it in such a way as to keep it from either a generating an excessively rigid order or

actually arises only if the programmer of the model system tunes it in such a way as to keep it from either generating an excessively rigid order or

Match 101 (1):
Reference (007628 .. 007687, of 13533):

Subject (019214 .. 019272, of 28080):

involves an intelligent programmer selecting certain parameters and excluding others that is inputting information Second Kauffman s model systems are not constrained by functional considerations and thus are not analogous to biological systems A system of interconnected lights governed by pre programmed rules may well settle into a small number of patterns within a much larger space of possibilities But

involves an intelligent programmer selecting certain parameters and excluding others that is inputting information Second Kauffman s model systems are not constrained by functional considerations and thus are not analogous to biological systems A system of interconnected lights governed by preprogrammed rules may well settle into a small number of patterns within a much larger space of possibilities But

Match 102 (1):
Reference (007689 .. 007749, of 13533):

Subject (019274 .. 019333, of 28080):

these patterns have no function and need not meet any functional requirements they have no specificity analogous to that present in actual organisms Instead examination of Kauffman s 1995 model systems shows that they do not produce sequences or systems characterized by specified complexity but instead by large amounts of symmetrical order or internal redundancy interspersed with aperiodicity or mere complexity

these patterns have no function and need not meet any functional requirements they have no specificity analogous to that present in actual organisms Instead examination of Kauffman s model systems shows that they do not produce sequences or systems characterized by specified complexity but instead by large amounts of symmetrical order or internal redundancy interspersed with aperiodicity or mere complexity

Match 103 (1):
Reference (007754 .. 007785, of 13533):

Subject (019335 .. 019366, of 28080):

Getting a law governed system to generate repetitive patterns of flashing lights even with a certain amount of variation is clearly interesting but not biologically relevant On the other hand a system

Getting a law governed system to generate repetitive patterns of flashing lights even with a certain amount of variation is clearly interesting but not biologically relevant On the other hand a system

Match 104 (1):
Reference (007795 .. 007807, of 13533):

Subject (019375 .. 019390, of 28080):

would model a biologically relevant self organizational process at least if such a

would model a biologically relevant self organizational process at least if the system produced such messages

Match 105 (1):
Reference (007826 .. 007845, of 13533):

Subject (019401 .. 019420, of 28080):

In any case Kauffman s systems do not produce specified complexity and thus do not offer promising models for explaining

In any case Kauffman s systems do not produce specified complexity and thus do not offer promising models for explaining

Match 106 (1):
Reference (007856 .. 007934, of 13533):

Subject (019450 .. 019527, of 28080):

Even so Kauffman suggests that his self organizational models can specifically elucidate aspects of the Cambrian explosion According to Kauffman 1995 199 201 new Cambrian animals emerged as the result of long jump mutations that established new body plans in a discrete rather than gradual fashion He also recognizes that mutations affecting early development are almost inevitably harmful Thus he concludes that body plans once established will not change and that any subsequent evolution must occur within an established

Even so Kauffman suggests that his self organizational models can specifi cally elucidate aspects of the Cambrian explosion According to Kauffman new Cambrian animals emerged as the result of long jump mutations that established new body plans in a discrete rather than gradual fashion 120 He also recognizes that mutations affecting early development are almost inevitably harmful Thus he concludes that body plans once established will not change and that any subsequent evolution must occur within an established

Match 107 (1):
Reference (007940 .. 007979, of 13533):

Subject (019530 .. 019568, of 28080):

And indeed the fossil record does show a curious from a neo Darwinian point of view top down pattern of appearance in which higher taxa and the body plans they represent appear first only later to be followed by the

And indeed the fossil record does show a curious from a Darwinian point of view top down pattern of appearance in which higher taxa and the body plans they represent appear first only later to be followed by the

Match 108 (1):
Reference (007981 .. 007990, of 13533):

Subject (019570 .. 019579, of 28080):

of lower taxa representing variations within those original body designs

of lower taxa representing variations within those original body designs

Match 109 (1):
Reference (008001 .. 008024, of 13533):

Subject (019580 .. 019603, of 28080):

Further as Kauffman expects body plans appear suddenly and persist without significant modification over time But here again Kauffman begs the most important question

Further as Kauffman expects body plans appear suddenly and persist without significant modification over time But here again Kauffman begs the most important question

Match 110 (1):
Reference (008028 .. 008165, of 13533):

Subject (019605 .. 019738, of 28080):

produces the new Cambrian body plans in the first place Granted he invokes long jump mutations to explain this but he identifies no specific self organizational process that can produce such mutations Moreover he concedes a principle that undermines the plausibility of his own proposal Kauffman acknowledges that mutations that occur early in development are almost inevitably deleterious Yet developmental biologists know that these are the only kind of mutations that have a realistic chance of producing large scale evolutionary change i e the big jumps that Kauffman invokes Though Kauffman repudiates the neo Darwinian reliance upon random mutations in favor of self organizing order in the end he must invoke the most implausible kind of random mutation in order to provide a self organizational account of the new Cambrian body plans Clearly his model is not sufficient

produced the new Cambrian body plans in the first place Granted he invokes long jump mutations to explain this but he identifies no specific selforganizational process that can produce such mutations Moreover he concedes a principle that undermines the plausibility of his own proposal Kauffman acknowledges that mutations that occur early in development are almost inevitably deleterious Yet developmental biologists know that these are the only kind of mutations that have a realistic chance of producing large scale evolutionary change that is the big jumps that Kauffman invokes Though Kauffman repudiates the neo Darwinian reliance upon random mutations in favor of self organizing order in the end he must invoke the most implausible kind of random mutation to provide a selforganizational account of the new Cambrian body plans Clearly his model is not sufficient

Match 111 (1):
Reference (008201 .. 008210, of 13533):

Subject (021759 .. 021772, of 28080):

pattern of sudden appearance and stasis in the fossil record

pattern of appearance and morphological isolation that is evident in the Cambrian fossil record

Match 112 (1):
Reference (008258 .. 008281, of 13533):

Subject (005296 .. 005321, of 28080):

According to punctuationalists natural selection functions more as a mechanism for selecting the fittest species rather than the most fit individual among a species

According to many punctuationalists natural selection functions more as a mechanism for selecting the most fit species rather than the most fit individual among a species

Match 113 (1):
Reference (008286 .. 008296, of 13533):

Subject (005323 .. 005333, of 28080):

morphological change should occur in larger more discrete intervals than it

morphological change should occur in larger more discrete intervals than traditional

Match 114 (1):
Reference (008344 .. 008405, of 13533):

Subject (005656 .. 005718, of 28080):

noted that the proposed mechanism of punctuated evolutionary change simply lacked the raw material upon which to work As Valentine and Erwin 1987 note the fossil record fails to document a large pool of species prior to the Cambrian Yet the proposed mechanism of species selection requires just such a pool of species upon which to act Thus they conclude that the

note that the proposed mechanism of punctuated evolutionary change simply would have lacked the raw material upon which to work As Valentine and Erwin note the fossil record fails to document a large pool of species prior to the Cambrian Yet the proposed mechanism of species selection requires just such a pool of species upon which to act Thus they conclude that the

Match 115 (1):
Reference (008344 .. 008410, of 13533):

Subject (005656 .. 005724, of 28080):

noted that the proposed mechanism of punctuated evolutionary change simply lacked the raw material upon which to work As Valentine and Erwin 1987 note the fossil record fails to document a large pool of species prior to the Cambrian Yet the proposed mechanism of species selection requires just such a pool of species upon which to act Thus they conclude that the mechanism of species selection probably

note that the proposed mechanism of punctuated evolutionary change simply would have lacked the raw material upon which to work As Valentine and Erwin note the fossil record fails to document a large pool of species prior to the Cambrian Yet the proposed mechanism of species selection requires just such a pool of species upon which to act Thus they conclude that the probability that species selection is a

Match 116 (1):
Reference (009161 .. 009171, of 13533):

Subject (020354 .. 020366, of 28080):

the problem of the origin of form and information since the

the problem of the origin of biological information exposes a deficiency in the

Match 117 (1):
Reference (009319 .. 009332, of 13533):

Subject (000491 .. 000502, of 28080):

candidates for explaining the origination of biological form or the information necessary to produce

can account for the origin of the biological information necessary to produce

Match 118 (1):
Reference (009344 .. 009353, of 13533):

Subject (020346 .. 020363, of 28080):

approach to the problem of the origin of form specifically

a vast space of combinatorial possibilities Analysis of the problem of the origin of biological information exposes a

Match 119 (1):
Reference (009997 .. 010007, of 13533):

Subject (000227 .. 000239, of 28080):

design as an explanation for the origin of the biological information

design hypothesis from consideration as an explanation for the origin of biological form

Match 120 (1):
Reference (010001 .. 010011, of 13533):

Subject (000493 .. 000503, of 28080):

for the origin of the biological information necessary to produce the

for the origin of the biological information necessary to produce the

Match 121 (1):
Reference (010175 .. 010187, of 13533):

Subject (000037 .. 000048, of 28080):

and Lewontin 1978 have long acknowledged that organisms appear to have been designed

and Richard Lewontin acknowledge that biological organisms appear to have been designed

Match 122 (1):
Reference (010193 .. 010207, of 13533):

Subject (000061 .. 000074, of 28080):

that what Ayala 1994 5 calls the obvious design of living things is only apparent

that what Francisco Ayala calls the obvious design of living things is only apparent

Match 123 (1):
Reference (010740 .. 010764, of 13533):

Subject (014093 .. 014117, of 28080):

and philosophy of science have shown that many scientific theories particularly in the historical sciences are formulated and justified as inferences to the best explanation

and philosophy of science have shown that many scientific theories particularly in the historical sciences are formulated and justified as inferences to the best explanation

Match 124 (1):
Reference (010776 .. 010801, of 13533):

Subject (014119 .. 014142, of 28080):

Historical scientists in particular assess or test competing hypotheses by evaluating which hypothesis would if true provide the best explanation for some set of relevant data

Historical scientists in particular assess competing hypotheses by evaluating which hypothesis would if true provide the best explanation for some set of relevant data

Match 125 (1):
Reference (010813 .. 010828, of 13533):

Subject (014143 .. 014158, of 28080):

Those with greater explanatory power are typically judged to be better more probably true theories Darwin

Those with greater explanatory power are typically judged to be better more probably true theories Darwin

Match 126 (1):
Reference (010831 .. 010884, of 13533):

Subject (014160 .. 014215, of 28080):

used this method of reasoning in defending his theory of universal common descent Moreover contemporary studies on the method of inference to the best explanation have shown that determining which among a set of competing possible explanations constitutes the best depends upon judgments about the causal adequacy or causal powers of competing explanatory entities

used this method of reasoning in defending his theory of universal common descent 85 Moreover contemporary studies on the method of inference to the best explanation have shown that determining which among a set of competing possible explanations constitutes the best depends upon judgments about the causal adequacy or causal powers of the competing explanatory entities

Match 127 (1):
Reference (010977 .. 010986, of 13533):

Subject (000227 .. 000239, of 28080):

design as an explanation for the origin of biological form

design hypothesis from consideration as an explanation for the origin of biological form

Match 128 (1):
Reference (010977 .. 010988, of 13533):

Subject (014620 .. 014631, of 28080):

design as an explanation for the origin of biological form and information

design is sufficient as a causal explanation for the origin of information

Match 129 (1):
Reference (011068 .. 011080, of 13533):

Subject (019810 .. 019830, of 28080):

of hierarchically arranged systems of parts In the first place intelligent human agents

of code or hierarchically arranged systems of parts Clearly they do In the first place we know that intelligent human agents

Match 130 (1):
Reference (011091 .. 011103, of 13533):

Subject (019794 .. 019810, of 28080):

power to produce information in the form of linear sequence specific arrangements of

powers sufficient to produce such increases in information either in the form of sequence specific lines of

Match 131 (1):
Reference (011099 .. 011120, of 13533):

Subject (019836 .. 019859, of 28080):

linear sequence specific arrangements of characters Indeed experience affirms that information of this type routinely arises from the activity of intelligent agents

source invariably comes to a mind that of a software engineer or programmer

source invariably we come to a mind to that of a programmer

Match 133 (1):
Reference (011171 .. 011201, of 13533):

Subject (019917 .. 019949, of 28080):

experience based knowledge of information flow confirms that systems with large amounts of specified complexity especially codes and languages invariably originate from an intelligent source from a mind or personal agent

experience based knowledge of information flow confirms that systems with large amounts of specified complexity especially codes and languages invariably originate from an intelligent source that is from a mind or personal agent

Match 134 (1):
Reference (011203 .. 011217, of 13533):

Subject (014501 .. 014512, of 28080):

Quastler 1964 put it the creation of new information is habitually associated with conscious activity

Quastler the creation of new information is habitually associated with conscious activity

Match 135 (1):
Reference (011226 .. 011237, of 13533):

Subject (020510 .. 020521, of 28080):

the highly specified hierarchical arrangements of parts in animal body plans also

the highly specified hierarchical arrangements of parts in animal body plans also

Match 136 (1):
Reference (011258 .. 011344, of 13533):

Subject (020524 .. 020613, of 28080):

At every level of the biological hierarchy organisms require specified and highly improbable arrangements of lower level constituents in order to maintain their form and function Genes require specified arrangements of nucleotide bases proteins require specified arrangements of amino acids new cell types require specified arrangements of systems of proteins body plans require specialized arrangements of cell types and organs Organisms not only contain information rich components such as proteins and genes but they comprise information rich arrangements of those components and the systems that comprise them

At every level of the biological hierarchy organisms require specified and highly improbable arrangements of lower level constituents in order to maintain their form and function Genes require specified arrangements of nucleotide bases proteins require specified arrangements of amino acids new cell types require specified arrangements of proteins and systems of proteins new body plans require specialized arrangements of cell types and organs Organisms not only contain information rich components such as proteins and genes but they comprise information rich arrangements of those components and the subsystems that comprise them

Match 137 (1):
Reference (011258 .. 011352, of 13533):

Subject (020524 .. 020616, of 28080):

At every level of the biological hierarchy organisms require specified and highly improbable arrangements of lower level constituents in order to maintain their form and function Genes require specified arrangements of nucleotide bases proteins require specified arrangements of amino acids new cell types require specified arrangements of systems of proteins body plans require specialized arrangements of cell types and organs Organisms not only contain information rich components such as proteins and genes but they comprise information rich arrangements of those components and the systems that comprise them Yet we know based on our present experience

At every level of the biological hierarchy organisms require specified and highly improbable arrangements of lower level constituents in order to maintain their form and function Genes require specified arrangements of nucleotide bases proteins require specified arrangements of amino acids new cell types require specified arrangements of proteins and systems of proteins new body plans require specialized arrangements of cell types and organs Organisms not only contain information rich components such as proteins and genes but they comprise information rich arrangements of those components and the subsystems that comprise them Based on experience

Match 138 (1):
Reference (011374 .. 011416, of 13533):

Subject (020641 .. 020688, of 28080):

in which both individual modules and the arrangements of those modules exhibit complexity and specificity information so defined Individual transistors resistors and capacitors exhibit considerable complexity and specificity of design at a higher level of organization their specific arrangement within an integrated circuit

in which both individual modules and also the hierarchical arrangements of those modules exhibit complexity and functional specificity information so defined Individual transistors resistors and capacitors exhibit considerable complexity and specificity of design at a higher level of organization their specific arrangement and connection within an integrated circuit

Match 139 (1):
Reference (011420 .. 011434, of 13533):

Subject (020686 .. 020704, of 28080):

and reflects further design Conscious and rational agents have as part of their powers of

an integrated circuit reflects further design Conscious and rational human agents have as a consequence of their powers of

Match 140 (1):
Reference (011471 .. 011484, of 13533):

Subject (020728 .. 020747, of 28080):

we have good reason to doubt that mutation and selection self organizational processes or

we have good reasons to doubt that either the mutation selection mechanism or self organizational processes can produce such information

Match 141 (1):
Reference (011524 .. 011533, of 13533):

Subject (000227 .. 000239, of 28080):

design as an explanation for the origin of biological form

design hypothesis from consideration as an explanation for the origin of biological form

Match 142 (1):
Reference (011524 .. 011535, of 13533):

Subject (014620 .. 014631, of 28080):

design as an explanation for the origin of biological form and information

design is sufficient as a causal explanation for the origin of information

Match 143 (1):
Reference (011537 .. 011553, of 13533):

Subject (019990 .. 020006, of 28080):

agents have just those necessary powers that natural selection lacks as a condition of its causal adequacy

agents have just those necessary powers that natural selection lacks as a condition of its causal adequacy

Match 144 (1):
Reference (011559 .. 011575, of 13533):

Subject (020014 .. 020027, of 28080):

previous analysis we saw that natural selection lacked the ability to generate novel information precisely because it

arisen Natural selection can favor new proteins and genes but only after they

arisen Natural selection can favor new proteins and genes but only after they

Match 146 (1):
Reference (011598 .. 011611, of 13533):

Subject (020053 .. 020066, of 28080):

some function The job of generating new functional genes proteins and systems of proteins

some function The job of generating new functional genes proteins and systems of proteins

Match 147 (1):
Reference (011614 .. 011689, of 13533):

Subject (020070 .. 020143, of 28080):

entirely to random mutations Yet without functional criteria to guide a search through the space of possible sequences random variation is probabilistically doomed What is needed is not just a source of variation i e the freedom to search a space of possibilities or a mode of selection that can operate after the fact of a successful search but instead a means of selection that a operates during a search before success and that b is

entirely random mutations Yet without functional criteria to guide a search through the space of possible sequences random variation is probabilistically doomed What is needed is not just a source of variation that is the freedom to search a space of possibilities or a mode of selection that can operate after the fact of a successful search but instead a means of selection that a operates during a search before success and b is

Match 148 (1):
Reference (011693 .. 011747, of 13533):

Subject (020142 .. 020201, of 28080):

about or knowledge of a functional target Demonstration of this requirement has come from an unlikely quarter genetic algorithms Genetic algorithms are programs that allegedly simulate the creative power of mutation and selection Dawkins and Kuppers for example have developed computer programs that putatively simulate the production of genetic information by mutation and natural selection

b is informed by knowledge of a functional target Demonstration of this requirement has come from an unlikely quarter genetic algorithms Genetic algorithms are programs that allegedly simulate the creative power of mutation and selection Richard Dawkins and Bernd Olaf Kuppers for example have developed computer programs that putatively simulate the production of genetic information by mutation and natural selection

Match 149 (1):
Reference (011767 .. 011859, of 13533):

Subject (020220 .. 020314, of 28080):

these programs only succeed by the illicit expedient of providing the computer with a target sequence and then treating relatively greater proximity to future function i e the target sequence not actual present function as a selection criterion As Berlinski 2000 has argued genetic algorithms need something akin to a forward looking memory in order to succeed Yet such foresighted selection has no analogue in nature In biology where differential survival depends upon maintaining function selection cannot occur before new functional sequences arise Natural selection lacks foresight What natural selection lacks intelligent selection

these programs only succeed by the illicit expedient of providing the computer with a target sequence and then treating relatively greater proximity to future function that is the target sequence not actual present function as a selection criterion 123 As David Berlinski has argued genetic algorithms need something akin to a forward looking memory in order to succeed 124 Yet such foresighted selection has no analogue in nature In biology where differential survival depends upon maintaining function selection cannot occur before new functional sequencing arises Natural selection lacks foresight What natural selection lacks intelligent selection

Match 150 (1):
Reference (011864 .. 011879, of 13533):

Subject (020317 .. 020328, of 28080):

design provides Rational agents can arrange both matter and symbols with distant goals in mind In

design provides Agents can arrange matter with distant goals in mind In

Match 151 (1):
Reference (012037 .. 012069, of 13533):

Subject (020352 .. 020383, of 28080):

Analysis of the problem of the origin of biological information therefore exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess

Analysis of the problem of the origin of biological information exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess

Match 152 (1):
Reference (012037 .. 012073, of 13533):

Subject (020352 .. 020387, of 28080):

Analysis of the problem of the origin of biological information therefore exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess Intelligent agents have foresight

Analysis of the problem of the origin of biological information exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess Agents do have foresight

Match 153 (1):
Reference (012037 .. 012090, of 13533):

Subject (020352 .. 020404, of 28080):

Analysis of the problem of the origin of biological information therefore exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess Intelligent agents have foresight Such agents can select functional goals before they exist They can devise or select material means to

Analysis of the problem of the origin of biological information exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess Agents do have foresight Agents can also select functional goals before they exist They can devise or select material means to

Match 154 (1):
Reference (012100 .. 012110, of 13533):

Subject (020416 .. 020426, of 28080):

and then actualize those goals in accord with a preconceived design

and then actualize those goals in accord with a preconceived design

Match 155 (1):
Reference (012128 .. 012184, of 13533):

Subject (020433 .. 020487, of 28080):

The causal powers that natural selection lacks almost by definition are associated with the attributes of consciousness and rationality with purposive intelligence Thus by invoking design to explain the origin of new biological information contemporary design theorists are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence Instead they are positing an entity

The causal powers that natural selection lacks almost by definition are associated with the attributes of consciousness rationality and purposive intelligence Thus by invoking intelligent design to explain the origin of new information design theorists are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence Instead they are positing an entity

Match 156 (1):
Reference (012186 .. 012205, of 13533):

Subject (020489 .. 020508, of 28080):

precisely the attributes and causal powers that the phenomenon in question requires as a condition of its production and explanation

precisely the attributes and causal powers that the phenomenon in question requires as a condition of its production and explanation

Match 157 (1):
Reference (012230 .. 012239, of 13533):

Subject (020822 .. 020832, of 28080):

the most causally adequate explanation for the origin of the

the best most causally adequate explanation for the origin of the

Match 158 (1):
Reference (012275 .. 012284, of 13533):

Subject (020354 .. 020366, of 28080):

the problem of the origination of biological form and the

the problem of the origin of biological information exposes a deficiency in the